That depends on the format of the missing fonts, your OS, and how you received the files (is there a Document fonts folder?).
THe OS is Windows 8.1. The message that comes up says "the document uses one or more fonts that are not available on your system, and substitute font will be used. A substitute ill be used until the original fonts become available"
What font is missing?
Was the original file also created on Win 8.1?
Does the message appear, when you save the INDD CS5.5 file on the SAME place as the original file was?
Where has been installed the original file? In the OS, in InDesign's private Font Folder or in the File's Document Fonts Folder?
What kine of fonts are missing? OTF? T1? TTF? DFONT?
Did the file come from a Mac user? If the fonts are Mac-format TT, T1 or .dfont you cannot use them even if they are available in the Document fonts folder (presuming there is one), nor will Windows T1 fonts work from that folder, though they could be installed.
Bottom line is you need Windows compatible fonts, either OpenType, Windows TrueType, or (if you are willing to install them) Windows Type 1. If those are not available already on your system, or in a document fonts folder supplied with the file, you need to get them.